Notes:
Summary plots - Sample strategy is on the y-axis and number of sites is on the x-axis. Each plot is paired by parameter level vertically and the values in the cells are the mean value across all of the simulations for that parameter level. Note that each average encompasses all of the other varying simulation parameters.
Full plots - Sample strategy is on the y-axis and number of sites is on the x-axis. Each plot represents a unique simulation and the values in the cells are the mean value across all of the 10 iterations of that simulation across all three unique landscape seeds (i.e., all three sets of Neutral Landscape Models) for a total of 30 replicates. For these plots: K = population size (not to be confused with the number of latent factors (K)), phi = selection strength, m = migration, H = spatial autocorrelation, r = correlation between environmental layers.
RAE - Ratio Absolute Error - is the absolute difference between the observed and expected estimate of the ratio of IBE to IBD (i.e. the coefficient of IBE divided by the coefficient of IBD)
Bias - bias was calculated by taking the mean difference between the observed and expected coefficients or ratios
RAE
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0003 | 8.0000 | 8.0000 | 1 | 15.3480K | 1531.810409 | 1.9 × 10−319*** |
| sampstrat | 0.1078 | 1.5728 | 0.5243 | 3 | 15.3480K | 100.385844 | 2.4 × 10−64*** |
| K | 0.0126 | 0.6090 | 0.6090 | 1 | 15.3480K | 116.601181 | 4.4 × 10−27*** |
| m | 0.0523 | 10.5133 | 10.5133 | 1 | 15.3480K | 2013.030919 | 0.0*** |
| phi | −0.0020 | 0.0155 | 0.0155 | 1 | 15.3480K | 2.971532 | 0.085 |
| H | 0.0096 | 0.3544 | 0.3544 | 1 | 15.3480K | 67.857541 | 1.9 × 10−16*** |
| r | −0.0090 | 0.3123 | 0.3123 | 1 | 15.3480K | 59.800103 | 1.1 × 10−14*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G*** | −0.0046 | 0.0016 | −2.7960 | 0.02658997*** |
| EG - R | −0.0009 | 0.0016 | −0.5319 | 0.95132229 |
| EG - T** | −0.0249 | 0.0016 | −15.0697 | 0.0** |
| G - R | 0.0037 | 0.0016 | 2.2641 | 0.10653142 |
| G - T** | −0.0202 | 0.0016 | −12.2737 | 0.0** |
| R - T** | −0.0240 | 0.0016 | −14.5378 | 0.0** |
| *** p < 0.05 | ||||
| ** p < 0.001 | ||||
RAE
Ratio Bias
IBD Bias
IBE Bias
RAE
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0054 | 10.9296 | 10.9296 | 1 | 8.6290K | 774.65997483 | 2.4 × 10−163*** |
| sampstrat | 0.2519 | 1.7532 | 0.8766 | 2 | 8.6290K | 62.13047517 | 1.6 × 10−27*** |
| K | 0.0003 | 0.0002 | 0.0002 | 1 | 8.6290K | 0.01177688 | 0.910 |
| m | 0.0196 | 0.8264 | 0.8264 | 1 | 8.6290K | 58.57599989 | 2.2 × 10−14*** |
| phi | −0.0053 | 0.0618 | 0.0618 | 1 | 8.6290K | 4.37735932 | 0.036** |
| H | 0.0115 | 0.2873 | 0.2873 | 1 | 8.6290K | 20.36485607 | 6.5 × 10−6*** |
| r | −0.0184 | 0.7299 | 0.7299 | 1 | 8.6290K | 51.73067018 | 6.9 × 10−13*** |
| *** p < 0.001 | |||||||
| ** p < 0.05 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | −0.0340 | 0.0031 | −10.8514 | 2.7 × 10−14*** |
| EG - R** | −0.0101 | 0.0031 | −3.2163 | 3.7 × 10−3** |
| EQ - R*** | 0.0239 | 0.0031 | 7.6351 | 8.6 × 10−14*** |
| *** p < 0.001 | ||||
| ** p < 0.01 | ||||
RAE
Ratio Bias
IBD Bias
IBE Bias
RAE
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0003 | 9.4335 | 9.4335 | 1 | 15.3430K | 8.826316e+02 | 1.2 × 10−188*** |
| sampstrat | 0.1099 | 0.7896 | 0.2632 | 3 | 15.3430K | 2.462613e+01 | 6.9 × 10−16*** |
| K | 0.0231 | 2.0533 | 2.0533 | 1 | 15.3430K | 1.921097e+02 | 2.0 × 10−43*** |
| m | 0.0799 | 24.4973 | 24.4973 | 1 | 15.3430K | 2.292047e+03 | 0.0*** |
| phi | −0.0003 | 0.0002 | 0.0002 | 1 | 15.3430K | 2.244788e-02 | 0.88 |
| H | 0.0020 | 0.0153 | 0.0153 | 1 | 15.3430K | 1.435012e+00 | 0.23 |
| r | −0.0057 | 0.1237 | 0.1237 | 1 | 15.3430K | 1.157134e+01 | 6.7 × 10−4*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G*** | −0.0135 | 0.0024 | −5.7327 | 5.9 × 10−8*** |
| EG - R*** | −0.0097 | 0.0024 | −4.0895 | 2.5 × 10−4*** |
| EG - T*** | −0.0198 | 0.0024 | −8.3745 | 4.1 × 10−14*** |
| G - R | 0.0039 | 0.0024 | 1.6429 | 0.35443857 |
| G - T** | −0.0062 | 0.0024 | −2.6417 | 0.04111055** |
| R - T*** | −0.0101 | 0.0024 | −4.2845 | 1.1 × 10−4*** |
| *** p < 0.001 | ||||
| ** p < 0.05 | ||||
RAE
Ratio Bias
IBD Bias
IBE Bias
Occasionally GDM fails to fit a model, in which case an NA value is assigned. Here we visualize the proportion of NAs (i.e., cases of failed fit) across the simulations:
Proportion of failed models:
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0064 | 14.4681 | 14.4681 | 1 | 8.3500K | 5.407432e+02 | 5.9 × 10−116*** |
| sampstrat | 0.3179 | 8.3211 | 4.1605 | 2 | 8.3500K | 1.554993e+02 | 5.0 × 10−67*** |
| K | 0.0000 | 0.0000 | 0.0000 | 1 | 8.3500K | 2.777680e-05 | 1.00 |
| m | 0.0231 | 1.1117 | 1.1117 | 1 | 8.3500K | 4.155104e+01 | 1.2 × 10−10*** |
| phi | −0.0049 | 0.0503 | 0.0503 | 1 | 8.3500K | 1.879243e+00 | 0.17 |
| H | 0.0007 | 0.0009 | 0.0009 | 1 | 8.3500K | 3.448557e-02 | 0.85 |
| r | −0.0137 | 0.3905 | 0.3905 | 1 | 8.3500K | 1.459672e+01 | 1.3 × 10−4*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | −0.0760 | 0.0044 | −17.3557 | 0.0*** |
| EG - R*** | −0.0272 | 0.0044 | −6.1624 | 2.1 × 10−9*** |
| EQ - R*** | 0.0488 | 0.0044 | 11.1986 | 7.3 × 10−15*** |
| *** p < 0.001 | ||||
RAE
Ratio Bias
IBD Bias
IBE Bias
Occasionally GDM fails to fit a model, in which case an NA value is assigned. Here we visualize the proportion of NAs (i.e., cases of failed fit) across the simulations:
Proportion of failed models: